10  Pseudobulk

Run reintegration after cleaning

Published

August 26, 2025

10.1 REINTEGRATION

The integrated scRNAseq dataset of all brain cell populations was subsetted to retain those cells no subsetted out by the “expert committee”.

10.2 PCA

PC details

  1. PC1 captures a strong myelination axis, with high loadings for oligodendrocyte and myelin-related genes (Plp1, Mbp, Mag, Mal, Car2, Cryab) and opposite contributions from astrocytic (Ptgds, Enpp2, Edil3) and microglial (Hexb, C1qa, Ctss, Cst3) markers.

  2. PC2 reflects a neuron–astrocyte interaction gradient, driven by the astrocytic ECM regulator Sparcl1 on one pole and the neuronal signaling gene Plcb1 on the other.

  3. PC3 highlights synaptic connectivity and neurotransmission, with neuronal adhesion and plasticity genes (Nrxn1, Ntm, Lsamp, Ctnnd2, Adgrb3, Ntrk2) and the inhibitory receptor Gabrb1 loading strongly, balanced by astrocytic transporters (Slc1a2, Slc4a4) and Ptprz1. Together, these axes describe complementary layers of variance corresponding to myelination, glial–neuronal signaling, and synaptic specialization.

10.3 UMAP after reintegration

10.4 Pseudobulk

10.4.1 Astrocytes

p_val avg_log2FC pct.1 pct.2 p_val_adj
Wdr17 1.0e-07 -0.6656742 1 1 0.0011904
Lpar1 1.0e-07 0.5192552 1 1 0.0012595
Dcc 1.0e-07 -0.6273549 1 1 0.0030505
Wif1 7.0e-07 0.1848369 1 1 0.0159661
Sorcs1 1.1e-06 0.3837130 1 1 0.0234440
Tmsb4x 1.8e-06 0.8196337 1 1 0.0383954
Tenm2 2.2e-06 0.3594390 1 1 0.0476388

10.4.2 BAM

p_val avg_log2FC pct.1 pct.2 p_val_adj
Cxcl13 0e+00 1.9569000 1 0.333 0.0002040
Wfdc17 2e-06 -0.8501451 1 1.000 0.0435564

10.4.3 Choroid

p_val avg_log2FC pct.1 pct.2 p_val_adj
Rgs2 0 0.9370808 1 1 0.00068

10.4.4 Endothelial

p_val avg_log2FC pct.1 pct.2 p_val_adj
Gria1 1e-07 0.2876162 1 1 0.0014814
Slc38a2 5e-07 -0.3942290 1 1 0.0101714

10.4.5 Ependymal

p_val avg_log2FC pct.1 pct.2 p_val_adj
Mt3 1e-07 -0.581966 1 1 0.0014678

10.4.6 Neurons

p_val avg_log2FC pct.1 pct.2 p_val_adj
Cldn5 0.0e+00 0.8740228 1.000 1.000 0.0000026
Ly6c1 0.0e+00 0.8417682 1.000 1.000 0.0000039
Hapln1 0.0e+00 -1.0575334 0.667 1.000 0.0000206
Slco1a4 0.0e+00 0.9098885 1.000 0.667 0.0000294
Ptprb 0.0e+00 0.7883225 1.000 0.667 0.0003976
Vgf 1.1e-06 0.8479086 1.000 1.000 0.0243259
Ly6a 1.6e-06 0.7068322 1.000 0.667 0.0353316

10.4.7 NPC

p_val avg_log2FC pct.1 pct.2 p_val_adj
Ikzf1 0.0e+00 1.0571115 1 1 0.0000004
Runx1 0.0e+00 1.3537906 1 1 0.0000057
Creg1 0.0e+00 1.0016099 1 1 0.0000301
Gpr183 0.0e+00 1.1165005 1 1 0.0000624
Adamts1 0.0e+00 0.9092272 1 1 0.0001537
Inpp5d 0.0e+00 1.1274030 1 1 0.0001906
Zfp36 0.0e+00 1.0025476 1 1 0.0003610
Lmo2 0.0e+00 0.9614975 1 1 0.0003979
Lrmda 0.0e+00 0.9927620 1 1 0.0009119
Fth1 1.0e-07 0.7754402 1 1 0.0015168
Sat1 1.0e-07 1.1250506 1 1 0.0016771
Lpcat2 1.0e-07 0.9794508 1 1 0.0017612
Unc93b1 1.0e-07 1.1107730 1 1 0.0018391
Nfkbia 1.0e-07 0.8980613 1 1 0.0019855
Tmem119 1.0e-07 0.8763570 1 1 0.0020384
Ptprc 2.0e-07 0.9292133 1 1 0.0042320
Lgals9 3.0e-07 0.7196859 1 1 0.0058081
Adap2 3.0e-07 0.8139424 1 1 0.0071801
P2ry12 6.0e-07 1.0277527 1 1 0.0118773
Cd83 7.0e-07 0.9920499 1 1 0.0145304
Itgam 7.0e-07 1.0216380 1 1 0.0145724
Abca9 8.0e-07 0.8031022 1 1 0.0174620
Rnase4 8.0e-07 0.8590141 1 1 0.0179884
Ly6e 8.0e-07 0.8554275 1 1 0.0180234
H2-T23 1.6e-06 0.7770506 1 1 0.0350168
Selplg 1.6e-06 0.7707752 1 1 0.0351740
Lyn 1.8e-06 0.9601579 1 1 0.0397079
St3gal6 2.1e-06 0.8886279 1 1 0.0453242

10.4.8 Oligodendrocytes

p_val avg_log2FC pct.1 pct.2 p_val_adj
Ms4a6b 5.0e-07 0.0686229 1 1 0.0096832
C1qa 8.0e-07 0.4272693 1 1 0.0167962
Shoc2 9.0e-07 -0.2455762 1 1 0.0196189
Ctss 1.2e-06 0.4387682 1 1 0.0254450
mt-Atp8 1.3e-06 -0.3642960 1 1 0.0273779
mt-Nd4l 2.0e-06 -0.4666682 1 1 0.0426910

10.4.9 OPC

p_val avg_log2FC pct.1 pct.2 p_val_adj
Hpgd 5e-07 -1.446021 1 1 0.0109219

10.4.10 T-cell

p_val avg_log2FC pct.1 pct.2 p_val_adj
Dscam 4e-07 0.8264654 1 1 0.008977

10.4.11 VMC

p_val avg_log2FC pct.1 pct.2 p_val_adj
Rbp4 0 1.454712 1 0.667 0.0003589